It's minor, but when I use this screen flag in a dungeon, activating it causes the screen's colors to warp. It's weird, and I have no clue what's going on.
Problem with using Whistle->Stairs screen flag in dungeons
It does it on the overworld too, It's done it as long as I can remember, I reported as a bug I think back in the 183.
You can get around it by just using the whistle to trigger a stair combo and not using the screen flag.
Whistle also made water walkable, I used this to cheat through Triforce of Heart.